not quite. We haven't acutally seen the EMS in action in the series yet unless you count madara's wierd timespace techniques as EMS abilities. Kishi might throw a curveball when it comes to the EMS later on... though I doubt it.
We don't know if his left eye is/was EMS or not.
He once had EMS, that's for sure (or so he said). But he actually may have lost it some way around. Even with his latest revelations, Itachi said he was a shadow of his former shelf... There must be a reason, and I guess it's his own EMS.
Gaining Senju's powers may have lost him his EMS as well in compensation? A more versatile ninja, losing his most specialized technique.
Another explanation: Konan said Madara had only five minutes before "reappearing". Maybe it's the eternal Izanagi, the fact you can use it as much as you want. But if you have to trick more than 5 minutes, you still have the possibility to lose your eye to survive.